RE: [DIYbio] Re: Primer Software?

I have the licensed version for my company but I really don't trust the primer Tm calculation since it does not use the "latest" calculation methods. If you take your primer made via snapgene and plug it into a more sophisticated program like Primer 3 Plus, which checks for hairpins, self annealing, and a ton of other user editable parameters, the Tm will vary from program to program. I've had issues designing primers via snapgene's minimalistic calculation approach. A few of my longer primers ~40bp failed. Later analysis with Primer 3 Plus showed a high chance of hairpin. When I redesigned it using only primer 3 it worked like a charm. I absolutely LOVE SnapGene but its trying to be jack of all trades. Even though I get my primers for a flat $5 a pop, its still a waste to have them fail due to silly avoidable design flaws...partly my own fault :P

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D